330.0
500
330
500.0
1050.0
77
61.0
false
14.0
179.0
138.0
125.0
false
47.0
189.0
204.0
131.0
false
48.0
189.0
2.0
filename
22.mml
date
1225669488000
url
http://mw2.concord.org/public/part2/diffat/22.mml
size
112698
codebase
/public/part2/diffat
define %waitingForCaBinding 1;
define %waitingForATPBinding 0;
define %waitingForATPSettling 0;
define %waitingForClearCavity 0;
define %waitingForProteinTransition 0;
define %waitingForCaSettling 0;
define %waitingForATPPocketFormation 0;
define %waitingForCaRelease 0;
define %waitingForFlashTransition 0;
define %waitingForProteinReset 0;
define %waitingForCaText 0;
define %formingATPSiteText 1;
define %waitingForATPText 2;
define %waitingForReactionText 3;
define %messagesOn 1;
define %topBlockerInPlace 1;
define %bottomBlockerInPlace 1;
define %topParticleIndex -1;
define %bottomParticleIndex -1;
define %caToCapture -1;
define %caToCaptureFar -1;
define %caToCaptureNear -1;
define %restraintSet 0;
define %caLeft 0;
define %caRight 0;
define %proteinX 17.2;
define %proteinY 11.3;
define %proteinImage 0;
define %endTransitionTime 0;
define %thisAtom 0;
define %atp1toCapture 0;
define %atp2toCapture 0;
define %bondToRemove 0;
define %partOfMolecule -1;
define %leftConc 0;
define %rightConc 0;
define %totalChemicalEnergy %number_of_molecules;
define %chemicalEnergy 0;
define %voltage 0;
define %leftConc 0;
define %rightConc 0;
define %i 0;
define %atpConc -1;
define %caConc -1;
define %leftWidth 18.6;
define %rightWidth %width-%leftWidth;
define %flashX 23.1;
define %flashY 20.7;
define %atpAtomX 24.9;
define %atpAtomY 20.8;
define %pocket1x 25;
define %pocket1y 19.9
define %pocket2x 25.9;
define %pocket2y 20.4
define %pocket3x 24.9;
define %pocket3y 20.9
define %pocket4x 24.5;
define %pocket4y 21.9;
define %rsurface1x 24;
define %rsurface1y 19.6;
define %rsurface2x 22.9;
define %rsurface2y 19.3;
define %rsurface3x 21.8;
define %rsurface3y 18.9;
define %rsurface4x 20.8;
define %rsurface4y 18.5;
define %rsurface5x 19.9;
define %rsurface5y 17.9;
define %rsurface6x 19.8;
define %rsurface6y 15.3;
define %rsurface7x 20.7;
define %rsurface7y 14.7;
define %rsurface8x 21.9;
define %rsurface8y 14.7;
define %rsurface9x 23;
define %rsurface9y 14.5;
define %rsurface10x 24;
define %rsurface10y 14.2;
define %nonATPsurfaceX 25;
define %nonATPsurfaceY 12.8;
define %lsurface1x 18.4;
define %lsurface1y 12.5;
define %lsurface2x 18.2;
define %lsurface2y 13.8;
define %lsurface3x 19.2;
define %lsurface3y 14.3;
define %lsurface4x 20.5;
define %lsurface4y 14.6;
define %lsurface5x 21.7;
define %lsurface5y 15.1;
define %lsurface6x 22.9;
define %lsurface6y 15.6;
define %lsurface7x 25.8;
define %lsurface7y 15.1;
define %lsurface8x 25.8;
define %lsurface8y 16.2;
define %lsurface9x 23;
define %lsurface9y 18.4;
define %lsurface10x 21.8;
define %lsurface10y 18.9;
define %lsurface11x 20.4;
define %lsurface11y 19.3;
define %lsurface12x 19;
define %lsurface12y 19.5;
define %lsurface13x 17.8;
define %lsurface13y 20.2;
define %lsurface14x 18.3;
define %lsurface14y 21.5;
define %flashImage 0;
define %obsLeftX 17.9;
define %obsRightX 23.6;
define %obsY 13.8;
define %obsWidth 1.4;
define %obsHeight 6.1;
define %leftObs 0;
define %rightObs 0;
define %rightObs2 0;
define %obsRight2x 25.3;
define %obsRight2y 14.6;
define %obsRight2width 0.8;
define %obsRight2height 2.2;
define %proteinAreaX 16;
define %proteinAreaY 12.7;
define %proteinAreaW 11.8;
define %proteinAreaH 8.2;
define %caCount 0;
define %atpCount 0;
define %atomsInProtein 0;
define %pAnchorX 26.6;
define %pAnchorY 18;
define %atpAnchor1x 26.4;
define %atpAnchor1y 22.2;
define %atpAnchor2x 25.4;
define %atpAnchor2y 25;
define %atpRestraintDeltaX 0.02;
define %atpRestraintDeltaY -0.42;
define %caRestraintX 21.1;
define %caRestraintY 16.3;
define %caRestraintDeltaX -0.08;
define %caRestraintDeltaY -0.01;
define %waitingForCa 0;
define %formingATP 1;
define %waitingForATP 2;
define %releasingATP 3;
define %watingForCaRelease 4;
define %restoringProtein 5;
define %waitingForCaText 0;
define %formingATPSiteText 1;
define %waitingForATP 2;
define %waitingForReaction 3;
capture ca ion
200
1 capture Ca
if (%waitingForCaBinding);
set %caToCaptureFar nearest(2,%caRestraintX,%caRestraintY,30);
set %caToCaptureNear nearest(2,%caRestraintX,%caRestraintY,1);
set %caToCapture %caToCaptureFar;
if ((%caToCaptureFar != -1) and (%atom[%caToCaptureFar].rx > %leftWidth));
if ((%caToCaptureNear != -1) and (%restraintSet) and (%caToCaptureNear == %caToCaptureFar));
set atom[%caToCapture].restraint 1000;
set atom[%caToCapture].restraint.x %caRestraintX;
set atom[%caToCapture].restraint.y %caRestraintY;
set atom[%caToCapture].friction 1;
set %waitingForCaBinding 0;
set %waitingForCaSettling 1;
set %restraintSet 0;
set %endTransitionTime "%model_time+400";
else;
if (%restraintSet == 0);
set %restraintSet 1;
set atom[%caToCapture].restraint 1;
set atom[%caToCapture].restraint.x %caRestraintX;
set atom[%caToCapture].restraint.y %caRestraintY;
endif;
endif;
endif;
endif;
wait for Ca to settle down then load next animation
100
2 settle Ca ion
If ((%waitingForCaSettling) and (%model_time > %endTransitionTime));
set %waitingForCaSettling 0;
set image[%formingATP].frame 1;
set image[%formingATP].loop 1;
set image[%formingATP].visible on;
set image[%waitingForCa].visible off;
set %thisAtom nearest(1, %atpAtomX, %atpAtomY);
select atom %thisAtom;
remove;
add atom 0 (%pocket1x, %pocket1y); select atom "%number_of_atoms-1"; set movable off;
add atom 0 (%pocket2x, %pocket2y); select atom "%number_of_atoms-1"; set movable off;
add atom 0 (%pocket3x, %pocket3y); select atom "%number_of_atoms-1"; set movable off;
add atom 0 (%pocket4x, %pocket4y); select atom "%number_of_atoms-1"; set movable off;
set movable off;
set %waitingForATPPocketFormation 1;
set %endTransitionTime "%model_time+2200";
endif;
waitng for atp pocket formation
100
3 waiting for ATP pocket
If ((%waitingForATPPocketFormation) and (%model_time > %endTransitionTime));
set %waitingForATPPocketFormation 0;
set %waitingForATPBinding 1;
endif;
wait for ATP capture
100
4 capture ATP
if (%waitingForATPBinding);
set %atpToCaptureFar nearestMolecule(%atpAnchor1x,%atpAnchor1y,20);
set %atpToCaptureNear nearestMolecule(%atpAnchor1x,%atpAnchor1y,2);
if (%atpToCaptureFar != -1);
set %atp1toCapture atomofmolecule(%atpToCaptureFar,0);
set %atp2toCapture atomofmolecule(%atpToCaptureFar,1);
if (%atom[%atp1toCapture].charge < 0);
set %atp1toCapture atomofmolecule(%atpToCaptureFar,1);
set %atp2toCapture atomofmolecule(%atpToCaptureFar,0);
endif;
if (%atpToCaptureNear != -1);
set atom[%atp1toCapture].restraint 20;
set atom[%atp1toCapture].restraint.x %atpAnchor1x;
set atom[%atp1toCapture].restraint.y %atpAnchor1y;
set atom[%atp1toCapture].friction 1;
set atom[%atp2toCapture].restraint 20;
set atom[%atp2toCapture].restraint.x %atpAnchor2x;
set atom[%atp2toCapture].restraint.y %atpAnchor2y;
set atom[%atp2toCapture].friction 1;
set %restraintSet 0;
set %waitingForATPBinding 0;
set %waitingForATPSettling 1;
set %endTransitionTime "%model_time+1600";
else;
if (%restraintSet == 0);
set %restraintSet 1;
set atom[%atp1toCapture].restraint 1;
set atom[%atp1toCapture].restraint.x %atpAnchor1x;
set atom[%atp1toCapture].restraint.y %atpAnchor1y;
set atom[%atp2toCapture].restraint 1;
set atom[%atp2toCapture].restraint.x %atpAnchor2x;
set atom[%atp2toCapture].restraint.y %atpAnchor2y;
endif;
endif;
endif;
endif;
wait for ATP to settle in place then initiate reaction
100
5 wait for ATP settling
If ((%waitingForATPSettling) and (%model_time > %endTransitionTime));
set %waitingForATPSettling 0;
set %waitingForClearCavity 1;
endif;
waitng for only one Ca in protein
50
6 waiting for clear cavity
If (%waitingForClearCavity);
set %caCount count(2,%proteinAreaX,%proteinAreaY,%proteinAreaW,%proteinAreaH);
set %atpCount count(3,%proteinAreaX,%proteinAreaY,%proteinAreaW,%proteinAreaH);
set %atomsInProtein "%caCount+%atpCount";
if (%atomsInProtein == 1);
set %waitingForClearCavity 0;
select element 0-1;
remove;
add obstacle (%obsRightX, %obsY, %obsWidth, %obsHeight);
set %rightObs "%number_of_obstacles-1";
set obstacle[%rightObs].visible off;
add obstacle (%obsRight2x, %obsRight2y, %obsRight2width, %obsRight2height);
set %rightObs2 "%number_of_obstacles-1";
set obstacle[%rightObs2].visible off;
set %waitingForFlashTransition 1;
set %endTransitionTime "%model_time+500";
add image flash.gif (%flashX,%flashY);
set %i 0;
endif;
endif;
open protein to release calcium
100
8 transition protein
If (%waitingForProteinTransition);
if (%model_time > %endTransitionTime);
set %waitingForProteinTransition 0;
select obstacle %leftObs;
remove;
set %rightObs %rightObs-1;
set %rightObs2 %rightObs2-1;
add atom 0 (%lsurface1x,%lsurface1y);
add atom 0 (%lsurface2x,%lsurface2y);
add atom 0 (%lsurface3x,%lsurface3y);
add atom 0 (%lsurface4x,%lsurface4y);
add atom 0 (%lsurface5x,%lsurface5y);
add atom 0 (%lsurface6x,%lsurface6y);
add atom 0 (%lsurface9x,%lsurface9y);
add atom 0 (%lsurface10x,%lsurface10y);
add atom 0 (%lsurface11x,%lsurface11y);
add atom 0 (%lsurface12x,%lsurface12y);
add atom 0 (%lsurface13x,%lsurface13y);
add atom 0 (%lsurface14x,%lsurface14y);
select element 0;
set movable off;
set atom[%caToCapture].restraint 0;
set atom[%caToCapture].friction 0;
set %waitingForCaRelease 1;
else;
%i++;
set atom[%caToCapture].restraint.x "%caRestraintX+%i*%caRestraintDeltaX";
set atom[%caToCapture].restraint.y "%caRestraintY+%i*%caRestraintDeltaY";
set atom[%atp1toCapture].restraint.x "%atpAnchor1x+%i*%atpRestraintDeltaX";
set atom[%atp1toCapture].restraint.y "%atpAnchor1y+%i*%atpRestraintDeltaY";
set atom[%atp1toCapture].rx "%atpAnchor1x+%i*%atpRestraintDeltaX";
set atom[%atp1toCapture].ry "%atpAnchor1y+%i*%atpRestraintDeltaY";
endif;
endif;
waiting for flash to finish
7 waiting for flash
If ((%waitingForFlashTransition) and (%model_time > %endTransitionTime));
set %waitingForFlashTransition 0;
set image[%releasingATP].frame 1;
set image[%releasingATP].loop 1;
set image[%releasingATP].visible on;
set image[%formingATP].visible off;
set %caToCapture nearest(2,%caRestraintX,%caRestraintY,2);
set %atp1toCapture nearest(3,%atpAnchor1x,%atpAnchor1y,2);
set %atp2toCapture nearesttoatom(3,%atp1toCapture,10,2);
set atom[%atp2toCapture].restraint 0;
set atom[%atp2toCapture].friction 0;
set %atpBond whichrbond(%atp1toCapture,%atp2toCapture);
select rbond %atpBond;
remove;
set %flashImage %number_of_images-1;
select image %flashImage;
remove;
add image adp.gif atomno=%atp2toCapture;
add image p.gif atomno=%atp1toCapture;
set %endTransitionTime "%model_time+1000";
set %waitingForProteinTransition 1;
endif;
waiting for ca release and clear protein
100
9 wating for ca release
If (%waitingForCaRelease);
set %atomsInProtein count(2,%proteinAreaX,%proteinAreaY,%proteinAreaW,%proteinAreaH);
if (%atomsInProtein == 0);
set %waitingForCaRelease 0;
select element 0;
remove;
add obstacle (%obsLeftX, %obsY, %obsWidth, %obsHeight);
set %leftObs "%number_of_obstacles-1";
set obstacle[%leftObs].visible off;
set image[%restoringProtein].frame 1;
set image[%restoringProtein].loop 1;
set image[%restoringProtein].visible on;
set image[%releasingATP].visible off;
set %atp1toCapture nearest(3,%pAnchorX,%pAnchorY);
set atom[%atp1toCapture].restraint 0;
set atom[%atp1toCapture].friction 0;
set atom[%atp1toCapture].vx 300;
set %waitingForProteinReset 1;
set %endTransitionTime "%model_time+1000";
endif;
endif;
revert to original shape
100
10 reset protein
If ((%waitingForProteinReset) and (%model_time > %endTransitionTime));
set %waitingForProteinReset 0;
set image[%waitingForCa].visible on;
set image[%restoringProtein].visible off;
select obstacle %rightObs2;
remove;
select obstacle %rightObs;
remove;
set %leftObs %leftObs-2;
add atom 0 (%rsurface1x,%rsurface1y);
add atom 0 (%rsurface2x,%rsurface2y);
add atom 0 (%rsurface3x,%rsurface3y);
add atom 0 (%rsurface4x,%rsurface4y);
add atom 0 (%rsurface5x,%rsurface5y);
add atom 0 (%rsurface6x,%rsurface6y);
add atom 0 (%rsurface7x,%rsurface7y);
add atom 0 (%rsurface8x,%rsurface8y);
add atom 0 (%rsurface9x,%rsurface9y);
add atom 0 (%rsurface10x,%rsurface10y);
select element 0;
set movable off;
set %topBlockerInPlace 0;
set %bottomBlockerInPlace 0;
set %waitingForCaBinding 1;
set %caToCapture -1;
endif;
add atom to block top of protein
100
add top blocker
if (%topBlockerInPlace != 1);
add atom 1 (%nonATPsurfaceX,%nonATPsurfaceY);
set %topParticleIndex nearest(1,%nonATPsurfaceX,%nonATPsurfaceY,1);
if (%topParticleIndex != -1);
set %topBlockerInPlace 1;
set atom[%topParticleIndex].movable off;
endif;
endif;
add bottom blocker
100
add bottom blocker
if (%bottomBlockerInPlace != 1);
add atom 1 (%atpAtomX,%atpAtomY);
set %bottomParticleIndex nearest(1,%atpAtomX,%atpAtomY,1);
if (%bottomParticleIndex != -1);
set %bottomBlockerInPlace 1;
set atom[%bottomParticleIndex].movable off;
endif;
endif;
update the graphs
100
update graphs
set %leftConc count(2,0,0,%leftWidth, %height);
set %leftConc %leftConc/(%leftWidth*%height);
set %rightConc count(2,%leftWidth,0,%rightWidth,%height);
set %rightConc %rightConc/(%rightWidth*%height);
set %chemicalEnergy %number_of_molecules;
set %voltage %totalChemicalEnergy-%chemicalEnergy;
store 1 %leftConc;
store 0 %rightConc;
store 2 %chemicalEnergy;
store 3 %voltage;
display messages
200
message handler
if (%messagesOn);
select textbox all;
set visible off;
select textbox none;
if (%waitingForCaBinding);
set textbox[%waitingForCaText].visible on;
endif;
if (%waitingForATPPocketFormation);
set textbox[%formingATPSiteText].visible on;
endif;
if (%waitingForATPBinding);
set textbox[%waitingForATPText].visible on;
endif;
if (%waitingForClearCavity);
set textbox[%waitingForReactionText].visible on;
endif;
endif;
1.0
None
-7179849
membraneBkgLarge.png
255
0
255
255
waitingForCa.gif
1
172.0
113.0
CaAtpaseFormATPSite.gif
1
1
false
172.0
113.0
waitingForATP.gif
1
2
false
172.0
113.0
CaAtpaseReleaseCa.gif
1
3
false
172.0
113.0
waitingForCaRelease.gif
1
4
false
172.0
113.0
CaAtpaseRestore.gif
1
5
false
172.0
113.0
atp.gif
-0.012577953
7
class org.concord.mw2d.models.RadialBond
1
6
324.0
234.0
atp.gif
0.2826795
class org.concord.mw2d.models.RadialBond
1
7
324.0
182.99999999999994
atp.gif
0.3845015
6
class org.concord.mw2d.models.RadialBond
1
8
251.0
280.0
atp.gif
-1.2924967
4
class org.concord.mw2d.models.RadialBond
1
9
242.0
28.0
atp.gif
0.61332756
3
class org.concord.mw2d.models.RadialBond
1
10
429.0
20.5
atp.gif
-0.31204212
5
class org.concord.mw2d.models.RadialBond
1
11
427.0
200.50000000000003
atp.gif
-0.47161558
2
class org.concord.mw2d.models.RadialBond
1
12
306.0
97.0
atp.gif
-0.14399642
1
class org.concord.mw2d.models.RadialBond
1
13
418.0
261.0
caIon.png
13
class org.concord.mw2d.models.Atom
1
14
390.0
43.0
caIon.png
17
class org.concord.mw2d.models.Atom
1
15
343.0
51.0
caIon.png
12
class org.concord.mw2d.models.Atom
1
16
298.27471676117176
55.57198516481955
caIon.png
23
class org.concord.mw2d.models.Atom
1
17
278.53866772599645
120.18598467623829
caIon.png
25
class org.concord.mw2d.models.Atom
1
18
407.0
191.0
caIon.png
15
class org.concord.mw2d.models.Atom
1
19
282.0
158.0
caIon.png
24
class org.concord.mw2d.models.Atom
1
20
406.0
89.0
caIon.png
26
class org.concord.mw2d.models.Atom
1
21
372.8722672612127
86.07573352996819
caIon.png
20
class org.concord.mw2d.models.Atom
1
22
408.7142463936035
125.57366514590686
caIon.png
19
class org.concord.mw2d.models.Atom
1
23
441.0852925911073
95.14195374929824
caIon.png
27
class org.concord.mw2d.models.Atom
1
24
461.2617007674528
86.38094207499648
caIon.png
16
class org.concord.mw2d.models.Atom
1
25
397.35864744776774
158.63188403795988
caIon.png
18
class org.concord.mw2d.models.Atom
1
26
300.0
258.0
caIon.png
22
class org.concord.mw2d.models.Atom
1
27
389.5
216.5
caIon.png
14
class org.concord.mw2d.models.Atom
1
28
381.03143403528264
266.59027834566615
caIon.png
21
class org.concord.mw2d.models.Atom
1
29
432.58883880080504
303.1880665640331
atp.gif
-0.31204212
8
class org.concord.mw2d.models.RadialBond
1
30
430.0
150.5
atp.gif
-0.31204212
9
class org.concord.mw2d.models.RadialBond
1
31
249.0
221.5
atp.gif
-0.31204212
10
class org.concord.mw2d.models.RadialBond
1
32
318.0
8.5
caIon.png
50
class org.concord.mw2d.models.Atom
1
33
466.0
121.0
caIon.png
53
class org.concord.mw2d.models.Atom
1
34
343.0
135.0
caIon.png
51
class org.concord.mw2d.models.Atom
1
35
394.5
14.5
caIon.png
56
class org.concord.mw2d.models.Atom
1
36
267.0
85.0
caIon.png
52
class org.concord.mw2d.models.Atom
1
37
420.5
50.5
caIon.png
55
class org.concord.mw2d.models.Atom
1
38
302.5
192.5
caIon.png
60
class org.concord.mw2d.models.Atom
1
39
391.0
301.0
caIon.png
58
class org.concord.mw2d.models.Atom
1
40
467.5
238.5
caIon.png
57
class org.concord.mw2d.models.Atom
1
41
416.5
246.5
caIon.png
59
class org.concord.mw2d.models.Atom
1
42
466.5
287.5
caIon.png
54
class org.concord.mw2d.models.Atom
1
43
341.5
303.5
caIon.png
73
class org.concord.mw2d.models.Atom
1
44
145.5
17.5
caIon.png
74
class org.concord.mw2d.models.Atom
1
45
83.5
25.5
caIon.png
61
class org.concord.mw2d.models.Atom
1
46
35.5
33.5
caIon.png
75
class org.concord.mw2d.models.Atom
1
47
67.5
59.5
caIon.png
62
class org.concord.mw2d.models.Atom
1
48
115.5
63.5
caIon.png
72
class org.concord.mw2d.models.Atom
1
49
148.5
93.5
caIon.png
63
class org.concord.mw2d.models.Atom
1
50
65.5
114.5
caIon.png
64
class org.concord.mw2d.models.Atom
1
51
5.5
93.5
caIon.png
76
class org.concord.mw2d.models.Atom
1
52
21.5
138.5
caIon.png
65
class org.concord.mw2d.models.Atom
1
53
35.5
174.5
caIon.png
66
class org.concord.mw2d.models.Atom
1
54
84.5
167.5
caIon.png
71
class org.concord.mw2d.models.Atom
1
55
136.5
145.5
caIon.png
70
class org.concord.mw2d.models.Atom
1
56
121.5
208.5
caIon.png
67
class org.concord.mw2d.models.Atom
1
57
136.5
265.5
caIon.png
68
class org.concord.mw2d.models.Atom
1
58
61.5
245.5
caIon.png
69
class org.concord.mw2d.models.Atom
1
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0
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false
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true
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255
1
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Waiting for binding
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true
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1
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Forming ATP
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true
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1
62
2
Waiting for binding
of ATP.
false
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true
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1
63
2
Waiting for reaction of
ATP with transport protein.
false
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1
false
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1
false
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false
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false
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false
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false
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false
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false
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false
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false
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false
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false
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